Last updated: 2024-11-01

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Knit directory: locust-comparative-genomics/

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    Modified:   data/list/HeadSAMER_nooutliers.txt
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    Modified:   data/list/HeadSCUBE_nooutliers.txt
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Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.

There are no past versions. Publish this analysis with wflow_publish() to start tracking its development.

1. Results mapping

STRATEGY 1: One genome S. gregaria

Mapping success

gregaria

#### Load our SRA metadata table
metaseq <- read_table("data/metadata/RNAseq_modified_METADATA2022.txt", col_names  = TRUE,  guess_max = 5000)

#### Create an interactive search table
metaseq %>%
    datatable(extensions = "Buttons", options = list(dom = "Blfrtip", buttons = c("copy",
        "csv", "excel"), lengthMenu = list(c(10, 20, 50, 100, 200, -1), c(10, 20,
        50, 100, 200, "All"))))

mycol_species <- c("green", "deeppink", "orange", "orange2", "blue2", "red2", "yellow2")

#### READS AVERAGE colored by STATUS
eren <- ggplot(metaseq, aes(x=Map_SUM, y = Inputtrim_reads, color = Species, label = SampleID))
eren <- eren + geom_point(size=2, alpha =0.7)
eren <- eren + scale_color_manual(values = mycol_species)
eren <- eren + theme_calc()
eren <- eren + geom_hline(yintercept=30000000, linetype="dotted", color = "green3")
eren <- eren + geom_hline(yintercept=50000000, linetype="dotted", color = "green3")
eren <- eren + geom_vline(xintercept=80, linetype="dotted", color = "blue2")
eren <- eren +  xlim(0,100)
options(scipen=20) #to remove the scientific annotation of the axis

#### make an interactive version of the scatter plot
attacktitan <- ggplotly(eren)
attacktitan

Figure XX: Interactive plot of the mapping rate success of each sample against their respective reference genome.

We added the green thresholds to indicate how many reads are recommended by Illumina (lower end and optimal). The blue line demonstrates where the mapping ratio could be considered not contaminated.


## READS AVERAGE colored by STATUS
mikasa <- ggplot(metaseq, aes(x=Map_SUM, y = Inputtrim_reads, color = Species, label = SampleID))
mikasa <- mikasa + geom_point(size=2, alpha =0.7)
mikasa <- mikasa + scale_color_manual(values = mycol_species)
mikasa <- mikasa + theme_calc()
mikasa <- mikasa + geom_hline(yintercept=30000000, linetype="dotted", color = "green3")
mikasa <- mikasa + geom_hline(yintercept=50000000, linetype="dotted", color = "green3")
mikasa <- mikasa + geom_vline(xintercept=80, linetype="dotted", color = "blue2")
mikasa <- mikasa +  xlim(0,100)
options(scipen=20) #to remove the scientific annotation of the axis

## make an interactive version of the scatter plot
attacktitan <- ggplotly(eren)
attacktitan

Figure XX: Interactive plot of the mapping rate success of each sample against gregaria genome.

We added the green thresholds to indicate how many reads are recommended by Illumina (lower end and optimal). The blue line demonstrates where the mapping ratio could be considered not contaminated.

piceifrons

cancellata

americana

cubense

nitens

STRATEGY 2: Own RefSeq genome

STAR reads mapping

This follows the same code as for STRATEGY 1 except that we will change the RefSeq to the transcript species genome path.

Mapping success

gregaria

piceifrons

cancellata

americana

cubense

nitens


sessionInfo()
R version 4.4.1 (2024-06-14)
Platform: aarch64-apple-darwin20
Running under: macOS Sonoma 14.7

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRblas.0.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.12.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: Asia/Tokyo
tzcode source: internal

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
 [1] vctrs_0.6.5       cli_3.6.3         knitr_1.48        rlang_1.1.4      
 [5] xfun_0.48         stringi_1.8.4     promises_1.3.0    jsonlite_1.8.9   
 [9] workflowr_1.7.1   glue_1.8.0        rprojroot_2.0.4   git2r_0.35.0     
[13] htmltools_0.5.8.1 httpuv_1.6.15     sass_0.4.9        fansi_1.0.6      
[17] rmarkdown_2.28    jquerylib_0.1.4   evaluate_1.0.1    tibble_3.2.1     
[21] fastmap_1.2.0     yaml_2.3.10       lifecycle_1.0.4   stringr_1.5.1    
[25] compiler_4.4.1    fs_1.6.5          Rcpp_1.0.13       pkgconfig_2.0.3  
[29] rstudioapi_0.17.1 later_1.3.2       digest_0.6.37     R6_2.5.1         
[33] utf8_1.2.4        pillar_1.9.0      magrittr_2.0.3    bslib_0.8.0      
[37] tools_4.4.1       cachem_1.1.0